G-quadruplex and i-motif are mutually exclusive in ILPR double-stranded DNA

G-quadruplex has demonstrated its biological functions in vivo. Although G-quadruplex in single-stranded DNA (ssDNA) has been well characterized, investigation of this species in double-stranded DNA (dsDNA) lags behind. Here we use chemical footprinting and laser-tweezers-based single-molecule approaches to demonstrate that a dsDNA fragment found in the insulin-linked polymorphic region (ILPR), 5'-(ACA GGGG TGT GGGG)2 TGT, can fold into a G-quadruplex at pH 7.4 with 100 mM K+, and an i-motif at pH 5.5 with 100 mM Li+. Surprisingly, under a condition that favors the formation of both G-quadruplex and i-motif (pH 5.5, 100 mM K+), a unique determination of change in the free energy of unfolding (ΔGunfold) by laser-tweezers experiments provides compelling evidence that only one species is present in each dsDNA. Under this condition, molecules containing G-quadruplex are more stable than those with i-motif. These two species have mechanical stabilities (rupture force≥17 pN) comparable to the stall force of RNA polymerases, which, from a mechanical perspective alone, could justify a regulatory mechanism for tetraplex structures in the expression of human insulin.     

Regulation of perforin activation and pre‐synaptic toxicity through C‐terminal glycosylation

Perforin is a highly cytotoxic pore‐forming protein essential for immune surveillance by cytotoxic lymphocytes. Prior to delivery to target cells by exocytosis, perforin is stored in acidic secretory granules where it remains functionally inert. However, how cytotoxic lymphocytes remain protected from their own perforin prior to its export to secretory granules, particularly in the Ca²⁺‐rich endoplasmic reticulum, remains unknown. Here, we show that N‐linked glycosylation of the perforin C‐terminus at Asn549 within the endoplasmic reticulum inhibits oligomerisation of perforin monomers and thus protects the host cell from premature pore formation. Subsequent removal of this glycan occurs through proteolytic processing of the C‐terminus within secretory granules and is imperative for perforin activation prior to secretion. Despite evolutionary conservation of the C‐terminus, we found that processing is carried out by multiple proteases, which we attribute to the unstructured and exposed nature of the region. In sum, our studies reveal a post‐translational regulatory mechanism essential for maintaining perforin in an inactive state until its secretion from the inhibitory acidic environment of the secretory granule.     

Quantitative trait loci (QTL) for reducing aflatoxin accumulation in corn

Aflatoxin produced by Aspergillus flavus in corn poses significant health risks to both humans and livestock. Exploitation of host-plant resistance in breeding programs is a sustainable way to minimize aflatoxin contamination. Identification of quantitative trait loci (QTL) associated with resistance to aflatoxin accumulation in kernels can accelerate development of aflatoxin-resistant corn using marker-assisted selection. An F_2:3 mapping population, developed from a cross involving a resistant inbred Mp715 and a susceptible inbred B73, was evaluated in replicated field trials with developing ears artificially inoculated with A. flavus for 2 years to identify QTL for reduced aflatoxin accumulation. Using composite interval mapping, 6 to 7 QTL for aflatoxin content were identified in both years with contribution of individual QTL ranging from <1 to 10% of phenotypic variation. More QTL were detected for husk coverage with phenotypic variance range of <1 to 16% explained by individual QTL. Both B73 and Mp715 alleles at these QTL loci contributed toward resistance. Husk coverage and aflatoxin levels were significantly correlated in both years. Our findings were further supported by overlapping of QTL for husk coverage ratings in four genomic regions on chromosomes 4, 8, and 10, where aflatoxin resistance QTL were reported in previous studies. Since most of the QTL were of low to moderate effects, pyramiding of these QTL may lead to enhanced resistance to aflatoxin accumulation in corn.     

Mitochondrial Ca2+ uptake in skeletal muscle health and disease

Muscle uses Ca²⁺ as a messenger to control contraction and relies on ATP to maintain the intracellular Ca²⁺ homeostasis. Mitochondria are the major sub-cellular organelle of ATP production. With a negative inner membrane potential, mitochondria take up Ca²⁺ from their surroundings, a process called mitochondrial Ca²⁺ uptake. Under physiological conditions, Ca²⁺ uptake into mitochondria promotes ATP production. Excessive uptake causes mitochondrial Ca²⁺ overload, which activates downstream adverse responses leading to cell dysfunction. Moreover, mitochondrial Ca²⁺ uptake could shape spatio-temporal patterns of intracellular Ca²⁺ signaling. Malfunction of mitochondrial Ca²⁺ uptake is implicated in muscle degeneration. Unlike non-excitable cells, mitochondria in muscle cells experience dramatic changes of intracellular Ca²⁺ levels. Besides the sudden elevation of Ca²⁺ level induced by action potentials, Ca²⁺ transients in muscle cells can be as short as a few milliseconds during a single twitch or as long as minutes during tetanic contraction, which raises the question whether mitochondrial Ca²⁺ uptake is fast and big enough to shape intracellular Ca²⁺ signaling during excitation-contraction coupling and creates technical challenges for quantification of the dynamic changes of Ca²⁺ inside mitochondria. This review focuses on characterization of mitochondrial Ca²⁺ uptake in skeletal muscle and its role in muscle physiology and diseases.     

Biocatalytic role of cytochrome P450s to produce antibiotics: A review

Cytochrome P450s belong to a family of heme-binding monooxygenases, which catalyze regio- and stereospecific functionalisation of C–H, C–C, and C–N bonds, including heteroatom oxidation, oxidative C–C bond cleavages, and nitrene transfer. P450s are considered useful biocatalysts for the production of pharmaceutical products, fine chemicals, and bioremediating agents. Despite having tremendous biotechnological potential, being heme-monooxygenases, P450s require either autologous or heterologous redox partner(s) to perform chemical transformations. Randomly distributed P450s throughout a bacterial genome and devoid of particular redox partners in natural products biosynthetic gene clusters (BGCs) showed an extra challenge to reveal their pharmaceutical potential. However, continuous efforts have been made to understand their involvement in antibiotic biosynthesis and their modification, and this review focused on such BGCs. Here, particularly, we have discussed the role of P450s involved in the production of macrolides and aminocoumarin antibiotics, nonribosomal peptide (NRPSs) antibiotics, ribosomally synthesized and post-translationally modified peptide (RiPPs) antibiotics, and others. Several reactions catalyzed by P450s, as well as the role of their redox partners involved in the BGCs of various antibiotics and their derivatives, have been primarily addressed in this review, which would be useful in further exploration of P450s for the biosynthesis of new therapeutics.     

Field-scale bioremediation of arsenic-contaminated groundwater using sulfate-reducing bacteria and biogenic pyrite

This research demonstrates that biogenic pyrite formed by stimulation of indigenous sulfate-reducing bacteria (SRB) in a natural aquifer can remove dissolved arsenic from contaminated groundwater under strongly reducing conditions. SRB metabolism led to the precipitation of biogenic pyrite nanoparticles capable of sorbing and co-precipitating arsenic. The field site is an industrial site where shallow groundwater in an unconfined sandy aquifer is contaminated by arsenic. Therefore, biodegradable organic carbon, ferrous iron, sulfate, and fertilizer were injected into groundwater and SRB metabolism began about 1 week later. Microscopic, X-ray diffraction, X-ray fluorescence, and electron microprobe analyses confirm the bio-mineralization of pyrite and over time, pyrite nanoparticles grew to form well-formed crystals (1–10?µm in diameter) or spherical aggregates that contain 0.05–0.4?wt. % arsenic, indicative of their capacity to sequester arsenic. Consequently, dissolved arsenic decreased from its initial concentration of 0.3–0.5?mg/L to below the regulatory clean-up standard for the site of 0.05?mg/L in three downgradient wells in a matter of weeks after injection. The main sequestration stage, with total arsenic removal rates greater than 90%, lasted for at least 6 months until the arrival and mixing of untreated groundwater from upgradient. Treated groundwater with most active bacterial sulfate reduction became enriched in heavy ³⁴S (range from 2.02 to 4.00 ‰) compared to unaffected well water (0.40–0.61 ‰). One to three orders of magnitude increases in SRB cells were observed in treated wells for at least 2?months after injection. For a full-scale remediation, the injection of solution should start at positions hydrologically upgradient from the major plume and proceed downgradient. If needed, aquifers may be repeatedly amended with biodegradable organic carbon to reestablish the reducing conditions that favor arsenic sequestration.     

Vulture distribution and people perception of vultures in Pokhara Valley,Nepal

Due to an abundance and diversity of vultures, Nepal is one of the most important countries for vulture conservation. Within Nepal, the Pokhara Valley is especially significant. We examine the distribution of vultures within the Pokhara Valley by conducting counts at 11 potential feeding or roosting sites using point count method. We further surveyed people of the valley regarding their perception of vulture ecology and conservation, knowledge of diclofenac use within the valley, and burial of livestock carcasses. We detected eight species of vultures, four of which are currently threatened with extinction. White‐rumped vulture Gyps bengalensis, Egyptian vulture Nephron percnopterus, and Himalayan vulture G. himalayensis were the most abundant. Almost all respondents (98%) had sighted the vultures in the wild. Formally educated respondents reported seeing vultures’ slightly more than nonformally educated respondents. Fifty‐eight percent respondents suspected habitat loss was the major threat for the vulture population decline in Pokhara Valley, and 97% respondents were not aware of any diclofenac use. The knowledge of vultures in people with different age groups suggests a more awareness programs are needed for local people, especially those who carry out animal husbandry and provide livestock to the vulture restaurant.     

Stable carbon and oxygen isotopes in human tooth enamel: Identifying breastfeeding and weaning in prehistory. Am. J. Phys. Anthropol. 106: 1–18.

ERRATUM: Wright LE and Schwarcz HP (1998) Stable Carbon and Oxygen Isotopes in Human Tooth Enamel: Identifying Breastfeeding and Weaning in Prehistory. Am. J. Phys. Anthropol. 106: 1–18. Isotopic ratios were incorrectly printed as percentages (%) rather than units permil (‰). Wherever “breast feeding” and “breast fed” occur, the words should be combined into “breastfeeding” and “breastfed” respectively. The correct information on isotopic ratios is the following: p. 1, Abstract: all % signs should be “‰”; p. 2, column two, last line: “… δ¹³C values¹, have been …”; p. 2, Footnote 1 should read: “Isotope ratios of carbon and oxygen are expressed in δ notation as follows, δ = [(R_sample/R_standard) − 1] × 1000, where R = ¹³C/¹²C for δ¹³C, and R = ¹⁸O/¹⁶O for δ¹⁸O, and are in units permil, ‰.”; p. 3, column two: all % signs should be “‰”, except for the 23rd line from the bottom, which reads: “… provided 95% of water intake by all infants …”; p. 5: all % signs should be “‰”; p. 6, column one: 8th and 9th line from bottom should be “… mean deviations were 0.029‰ for δ¹³C and 0.024‰ for δ¹⁸O …”; p. 6, column one: 2nd line from bottom should be “… only 0.208‰ for δ¹³C and only 0.091‰ for δ¹⁸O …”; p. 6, column two: top line: “… of 0.5‰ in δ¹³C and 0.2‰ in δ¹⁸O …”; p. 8, 9 and 10: all % signs should be “‰”; p. 11, column two: 7th line from top: “… the lipids are 4-6‰ lighter …”; p. 12, 13 and 14: all % signs should be “‰.”     

Permanent Genetic Resources added to the Molecular Ecology Resources Database 1 February 2010-31 March 2010

This article documents the addition of 228 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Anser cygnoides, Apodemus flavicollis, Athene noctua, Cercis canadensis, Glis glis, Gubernatrix cristata, Haliotis tuberculata, Helianthus maximiliani, Laricobius nigrinus, Laricobius rubidus, Neoheligmonella granjoni, Nephrops norvegicus, Oenanthe javanica, Paramuricea clavata, Pyrrhura orcesi and Samanea saman. These loci were cross-tested on the following species: Apodemus sylvaticus, Laricobius laticollis and Laricobius osakensis (a proposed new species currently being described).